Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 197 to 246 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		red
    		green
    		network_comparison
    99 no value jun dimerization protein. [refseq;acc:nm_130469] Subtracted 204.641 160.957 43.684
    melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Divided 88.2482 110.265 1.24949
    100 FOSL2 fos-related antigen 2. [swissprot;acc:p15408] Subtracted 204.641 161.046 43.595
    MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Divided 88.2482 110.265 1.24949
    101 FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Subtracted 204.641 161.051 43.59
    MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Divided 88.2482 110.265 1.24949
    102 FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Subtracted 204.642 161.068 43.574
    MAGED2 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Divided 88.2482 110.265 1.24949
    103 JUNB transcription factor jun-b. [swissprot;acc:p17275] Subtracted 201.144 158.868 42.276
    TRO trophinin. [swissprot;acc:q12816] Divided 88.2482 110.265 1.24949
    104 HOMER2 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 252.371 202.016 1.24926
    TARDBP tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Subtracted 256.228 298.438 42.21
    105 GNB1 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Divided 266.716 333.165 1.24914
    JUND transcription factor jun-d. [swissprot;acc:p17535] Subtracted 200.941 158.941 42
    106 COQ7 ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Divided 252.329 202.004 1.24913
    NOSTRIN nostrin. [refseq;acc:nm_052946] Subtracted 209.299 249.187 39.888
    107 HOMER1 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Divided 252.309 201.998 1.24907
    SNF8 eap30 subunit of ell complex. [refseq;acc:nm_007241] Subtracted 209.299 249.187 39.888
    108 HOMER3 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Divided 252.296 201.995 1.24902
    SLC39A6 liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Subtracted 209.299 249.187 39.888
    109 GAD2 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]
    GNB4 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Divided 266.933 333.281 1.24856
    110 DTX2 deltex 2. [refseq;acc:nm_020892] 333.144 267.393 1.2459
    NAPG gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Subtracted 209.299 249.187 39.888
    111 DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Divided 332.925 267.274 1.24563
    GAD1 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Subtracted 209.299 249.187 39.888
    112 PBK t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Divided 332.874 267.246 1.24557
    POLE4 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Subtracted 275.754 235.908 39.846
    113 KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Divided 332.874 267.246 1.24557
    PPP2CA serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Subtracted 194.372 234.204 39.832
    114 B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 229.818 267.265 37.447
    KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Divided 332.874 267.246 1.24557
    115 HAT1 histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Subtracted 277.546 240.461 37.085
    KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Divided 332.874 267.246 1.24557
    116 GNB3 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] 268.565 334.483 1.24545
    HMG20B high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Subtracted 208.52 171.595 36.925
    117 HMG20A high-mobility group 20a. [refseq;acc:nm_018200] 208.588 171.778 36.81
    NEURL neuralized-like. [refseq;acc:nm_004210] Divided 332.326 266.948 1.24491
    118 NDUFA12 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] 284.753 228.934 1.24382
    OSR1 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Subtracted 274.027 237.79 36.237
    119 ADIPOR2 adiponectin receptor 2. [refseq;acc:nm_024551] 281.582 246.371 35.211
    NDUFS4 nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Divided 318.982 259.004 1.23157
    120 KCND2 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 269.278 327.709 1.21699
    TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Subtracted 227.199 192.715 34.484
    121 CTH cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Divided 269.254 327.655 1.2169
    TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Subtracted 227.202 192.823 34.379
    122 COPS3 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] 199.949 234.187 34.238
    KCND3 potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Divided 269.248 327.642 1.21688
    123 KCND1 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] 269.23 327.601 1.21681
    SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Subtracted 227.032 193.056 33.976

    Legend:
    - Rank is the rank after comparing the two networks
    - Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
    - Hugo is the HGNC identifier if it exists
    - Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
    - Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
    - Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
    - Filtered specifies whether we only included the high confidence microarry measurements or not.
    - http://analysis.yellowcouch.org/